-
Notifications
You must be signed in to change notification settings - Fork 4
Expand file tree
/
Copy pathnextflow_schema.json
More file actions
277 lines (277 loc) · 15.3 KB
/
nextflow_schema.json
File metadata and controls
277 lines (277 loc) · 15.3 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/nf-core/seqsubmit/main/nextflow_schema.json",
"title": "nf-core/seqsubmit pipeline parameters",
"description": "Submit sequences, assemblies, MAGs, etc., to public archives",
"type": "object",
"$defs": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["outdir", "input"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "Path to comma-separated file describing the data to be submitted. Format depends on the pipeline mode (mags/bins/metagenomic_assemblies).",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with a set of columns depending on the type of data being submitted. See [usage docs](https://nf-co.re/seqsubmit/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
}
}
},
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
"description": "Git commit id for Institutional configs.",
"default": "master",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
"type": "string",
"description": "Institutional config name.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_description": {
"type": "string",
"description": "Institutional config description.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_contact": {
"type": "string",
"description": "Institutional config contact information.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_url": {
"type": "string",
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"max_multiqc_email_size": {
"type": "string",
"description": "File size limit when attaching MultiQC reports to summary emails.",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
"fa_icon": "fas fa-image",
"hidden": true
},
"multiqc_methods_description": {
"type": "string",
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
"fa_icon": "fas fa-cog"
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"pipelines_testdata_base_path": {
"type": "string",
"fa_icon": "far fa-check-circle",
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"hidden": true
},
"trace_report_suffix": {
"type": "string",
"fa_icon": "far calendar",
"description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
"hidden": true
},
"help": {
"type": ["boolean", "string"],
"description": "Display the help message."
},
"help_full": {
"type": "boolean",
"description": "Display the full detailed help message."
},
"show_hidden": {
"type": "boolean",
"description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
}
}
},
"pipeline_options": {
"title": "Pipeline flow control parameters",
"type": "object",
"description": "Use these parameters to control the flow of the pipeline execution.",
"required": ["centre_name", "mode"],
"properties": {
"centre_name": {
"type": "string",
"description": "The center name of the submitter (mandatory for broker accounts).",
"help": "ena-webin-cli argument -centerName: the center name of the submitter (mandatory for broker accounts)."
},
"upload_tpa": {
"type": "boolean",
"description": "Flag to control the type of assembly study (third party assembly or not)",
"default": false,
"help": "Use this flag if the study is a third party assembly (TPA). Default: false"
},
"mode": {
"type": "string",
"default": null,
"description": "Type of upload",
"help_text": "Different types of data require specific upload steps. That mode controls what upload workflow to run depending on type of data (mags/bins/metagenomic_assemblies)",
"enum": ["mags", "bins", "metagenomic_assemblies"]
},
"test_upload": {
"type": "boolean",
"description": "Upload to TEST server instead of LIVE",
"default": true,
"help": "Use that flag for development purposes or for validation of your submissions. Submission would be done to TEST ENA server instead of LIVE server. TEST server holds data 24h and removes afterwords. LIVE server does not have option to modify your submission, you can only suppress data and re-upload"
},
"upload_force": {
"type": "boolean",
"description": "Flag to control upload retries",
"default": true,
"help": "Forces reset of sample xmls generation. This is useful if you changed something in your tsv table, or if ENA metadata haven't been downloaded correctly (you can check this in ENA_backup.json). Default: true"
},
"submission_study": {
"type": "string",
"description": "ENA study accession (PRJ/ERP) to submit the data to",
"help_text": "Current implementation of pipeline requires to pre-register ENA project (PRJ/ERP) where you want to upload data to. Documentation how to register study: https://ena-docs.readthedocs.io/en/latest/submit/study.html"
},
"library": {
"type": "string",
"enum": ["metagenome", "metatranscriptome"],
"description": "Type of library for the submission. Required for creation of the new submission study.",
"help_text": "Uses script register_study from assembly_uploader package that requires this parameter to compose study title."
},
"ena_raw_reads_study_accession": {
"type": "string",
"description": "ENA study accession (PRJ/ERP) of the raw reads study associated with the assembly submission. Required for creation of the new submission study.",
"help_text": "Uses script register_study from assembly_uploader package that requires this parameter to compose study title and description."
},
"webincli_submit": {
"type": "boolean",
"description": "Submit or validate",
"default": true,
"help": "Flag to run submission or validation. Submission (true) will run upload of data with ena-webin-cli. Validation (false) validates correctness of input files, it does not do submission. Default: true (submit)"
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/generic_options"
},
{
"$ref": "#/$defs/pipeline_options"
}
]
}